OrgaCount - Setup

OrgaCount is a very flexible application that can be set up indiviually for most of the included features, such as counting and keyboard layout, species list and biovolumes. $name

Counting layout

By default, OrgaCount comes with an array of user-friendly counting layouts, which may be modified to meet the requirements of different projects und users.

The counting layout refers to the list of items (taxa, size classes of taxa, or items that are not organisms) that are counted during a counting session. Each item contains elements used for accomplishing the counting: the name of a taxon, details on its size class (in the case of predefined size classes), the keyboard button it relates to, a textbox with the count value, and other controls for individual counting settings.

OrgaCount comes with several design templates that can be selected in order to customise items in your counting layout. Switching to a different design can easily be done without restarting the programme, even in the middle of a counting process.

In the image above, a design template is displayed that also includes taxon icons. This feature may ease the localisation of items in the counting layout, and help new users becoming familiar with the different taxonomic subjects. The image icons can be uploaded via the 'Upload images' function. The images can have various sizes and are easily integrated into the counting layout:

The following list gives an overview over the features and advantages related with the flexible counting layout:
  • The application comes with an array of user friendly counting layouts
  • The list of counting layouts may be extended to meet the requirements of different users
  • Counting layouts are defined in HTML templates (design templates)
  • They can be modified by a person with limited computer skills
  • Counting layout may be changed at any time during counting session, it is not necessary to stop the counting process itself
  • For an item, a counting layout may include

    • an icon with its size defined in a templates
    • the name of taxon & size class
    • a button with key for counting
    • the counting value (by case for taxon or size class)
    • the counting factor
    • the counting area unit (stripe, chamber, quadrate etc)
    • a link for customisation panel used for changing
      • a CF tag (at taxon and size class level)
      • the freeze counting status and key used
    • a button for opening window for calculating biovolumes (in case of ad-hoc counting strategy)

  • When more than one size class are defined for an item, a popup window appears ( biovolumes or counting popup) with the list of counting size classes
  • OrgaCount comes with a full-screen mode. In full-screen mode, the application may display all or most of counting items within the visible area of the screen; no scrolling is necessary. Items may be enlarged making characters legible if screen is far from microscope. Running in full-screen mode eliminates details of the programme interface allowing focussing on counting task alone

Keyboard layout

OrgaCount allows you to select one of a variety of different keyboard layouts, which mainly differ according to various country features and languages. Depending on the language of the relevant keyboard, some of the keys in the keyboard layouts may not be available. It may therefore be useful to switch to a relevant keyboard layout which lists more items in your counting layout.
Keys that are not used in the current counting layout are displayed with white background colour. Used keys are displayed in blue. If there are keys that are used in your current counting layout, but not available on the chosen keyboard type, these are marked in red. You can use this feature as an easy way to see which keys are available.

The keyboard layout may be changed at any time during counting and does not affect your counting results.

The template design and keyboard layout are automatically inherited from previous counting sessions or from default settings of OrgaCount. In addition, you may choose either to remain with the existing settings, or personalize these.

The main features of the keyboard layout:
  • Counting can be done both by clicking on appropriate buttons in interface or by pressing appropriate keys (key input)
  • The system can store various keyboard layouts
  • The keyboard layout may be changed at any time during the counting session without affecting the results
  • Keys not present in current keyboard layout are visibly marked in interface
  • Items for which a key is not defined are visibly marked in the interface
  • Existence of design templates as already described with the counting layout

Counting list and items

The Counting (species) list module serves to populate the counting layout with items (usually taxa and/or size classes). Taxa selections for the counting layout are kept in virtual containers called 'Counting lists'. OrgaCount allows the management of multiple Counting lists, including the creation of new lists and the modification of existing lists. In OrgaCount, it is possible to switch to another Counting list during one and the same counting session. This extends the number of taxa (and size classes) that can be counted. Counting lists may also be reused from sample to sample.

One of the most versatile features of OrgaCount is its ability to include both taxa and size classes in the counting layout; thus allowing for an increased number of items. One and the same taxon item may relate to several size classes. If one of these is counted during a counting session, a size class popup appears by which you can select a size class.

The Counting list module may be easily accessed by expanding the respective branch under 'Current session':

The opening windows for the Counting list is organized in two major sections: A list of taxa selected for counting is located on left side of the module.
On the right side, you will see a list of all species available for the current counting domain. This list includes both taxon names and their authorship, and furthermore, has got a search function which you can use to search for taxa by alphabetical order:

If any counting lists have been defined, they can be selected from a pick list at the top of the left panel. OrgaCount will load the items of the selected list into your counting layout as well as to the left side of the panel of the Counting list module.

The following list summarises the features of the Counting list module:
  • The array of items in the counting interface may include both taxa and size classes
  • The array of items in the counting interface (e.g. taxa or size classes) may be changed by adding, removing listed species at any time during the counting session
  • When selecting items to be loaded in the interface, the system indicates if a certain taxon or size class has got data counted already in current counting session or at project level
  • If predefined size classes strategy is used, the system automatically detects if a taxon has only one size class and adds its size class as item in counting layout
  • Also provided are functions for

    • searching taxa (with alphabetic index)
    • listing predefined classes
    • adding new taxa
    • adding a new size class
    • deleting an existing size class
    • defining new arrays of items (new species lists)

  • An array of items may be used with any type of counting layout
  • The user can define lists of species by interest (i.e. taxonomic domain) and can switch between these lists at any time
  • OrgaCount comes with a tabular view of species list and their size classes. This list may be edited in-place directly in the data grid or may be exported to Excel. The tabular view comes with functions for filtering data by taxon name, date of entering for taxa and/or of size classes. Filtered lists may be exported in Excel.

Biovolume popup

The Biovolume Popup is a module used to define size classes during the counting process. It serves to render statistics necessary for calculating the biovolume of a taxon within a sample.
Most taxa have a relevant geometric form associated to them. If this is not the case (for instance, in the case of certain higher taxa which occur in more than one geometric form), you will be able to select one. For that purpose, you can access the biovolume popup by clicking on the Volume (V) button next to each of the items in your counting layout:

You will then see the biovolume popup with the main elements:
  • the taxon name
  • a diagram showing the volumetric shape of the taxon and its measurements
  • the name of the volumetric shape and its formula
  • a form for measuring cell dimensions for the taxon
  • a list of the items measured
  • various statistics for biovolume calculations, generated from the cells measured

If no geometric form is assigned to the taxon, you will have an additional alternative: By clicking on the V button you will open a pick list.

In the field labelled 'tags' you can now add additional information, which will be displayed in your counting layout.

The characteristics of the biovolume module as an overview:

  • If the predefined size classes counting strategy is used, the counting popup will automatically show a list of size classes by taxon
  • The 'size class key' can be counted by clicking on the button in the interface or by pressing an assigned key
  • The counting popup for predefined size class mode includes a list with taxon names, size range, counting unit, volume shape name, values for various measurements, calculated volume and calculated carbon
  • In the Ad-hoc counting mode, a module for calculating statistics and biovolumes is provided. This module presents the geometric shape name, formula used for calculations, and an illustration with measurements that have to perform when counting size classes
  • The form allows user to define keys for size classes
  • When a size class is counted, the application automatically does all biovolume statistical calculations:

    • counting of size classes
    • calculating average measurements for each dimension
    • calculating the biovolume for each size class in part
    • calculating average volume information based on volumes calculated for each size class in part
    • calculating average volume information by using measurement data for all values and counts stored during counting session

  • Volume formulas may be changed in the database; changes as well as additions are allowed
  • Biovolumes may be calculated during the counting session or at a later stage


OrgaCount is a very user-friendly and ease-to-use system. But also the technical requirements for setting up and operating the application are not restrictive and offer a wide range of possible installation modes. In the following, you will find a short overview.

Technical Information

OrgaCount is a web application that runs in a server environment. It uses technology that can be run on a wide variety of operating systems, including various editions of Linux and Windows. The web-based version of this application is preferably served on the AquaEcology server, and is continuously maintained using most recent updates. The database is also backed up regularly. Installation and usage of OrgaCount run through a secure port (https), which is vital to protecting your user login information as well as your data. Alternatively, OrgaCount may be installed on a customer's server system or used locally, running on any hard drive, compact flash or SD card.

The local version of OrgaCount also runs a local Apache server with PHP and MySQL, but it does not require any installation (Windows only). The database used by OrgaCount is MySQL, one of the fastest and most reliable database systems on the market. Any data produced with this application may be accessed easily, also beyond the current functionality of OrgaCount.


In order to run the web-based version of OrgaCount, you only need a standard web browser. The application is optimised for Firefox 3 or higher or Google Chrome 8 or higher. The Internet Explorer 7 or higher, as well as Opera 10 or higher were also some of the browsers used for testing OrgaCount, but could have some limitations at some points. However, the application also works with other types and versions of web browsers. We recommend using Firefox, which is currently the most reliable web browser available.

User System

The web-based version of OrgaCount can be used by several users at the same time. Standard users can only inspect their personal counting data. Project administrators, however, may view the data of other users in the team, as well. In order to use OrgaCount, you just sign in at the panel's login on the left side. The settings of the application will be user-specifically adjusted and provide every user with his individual work environment.

Menu Setup

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